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Opened 7 months ago
Closed 7 months ago
#17131 closed defect (duplicate)
Crash on Mac waking from sleep
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | normal | Milestone: | |
| Component: | Window Toolkit | Version: | |
| Keywords: | Cc: | ||
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
The following bug report has been submitted:
Platform: macOS-14.6.1-arm64-arm-64bit
ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC)
Description
Last time you used ChimeraX it crashed.
This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX.
Fatal Python error: Segmentation fault
Thread 0x00000003110f7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 579 in _handle_results
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x00000003100eb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 531 in _handle_tasks
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030f0df000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/selectors.py", line 415 in select
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/connection.py", line 930 in wait
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 502 in _wait_for_updates
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 522 in _handle_workers
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030e0d3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030d0c7000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030c0bb000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030b0af000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030a0a3000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000309097000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030808b000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x000000030707f000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000306073000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Thread 0x0000000305067000 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/multiprocessing/pool.py", line 114 in worker
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 975 in run
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 1038 in _bootstrap_inner
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/threading.py", line 995 in _bootstrap
Current thread 0x00000001f2858f40 (most recent call first):
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/ui/gui.py", line 330 in event_loop
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1054 in init
File "/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/chimerax/core/__main__.py", line 1217 in
File "", line 88 in _run_code
File "", line 198 in _run_module_as_main
Extension modules: chimerax.arrays._arrays, numpy.core._multiarray_umath, numpy.core._multiarray_tests, numpy.linalg._umath_linalg, numpy.fft._pocketfft_internal, numpy.random._common, numpy.random.bit_generator, numpy.random._bounded_integers, numpy.random._mt19937, numpy.random.mtrand, numpy.random._philox, numpy.random._pcg64, numpy.random._sfc64, numpy.random._generator, chimerax.geometry._geometry, PyQt6.QtCore, PyQt6.QtGui, PyQt6.QtWidgets, PyQt6.QtNetwork, PyQt6.QtPrintSupport, PyQt6.QtWebChannel, PyQt6.QtWebEngineCore, PyQt6.QtWebEngineWidgets, chimerax.atomic_lib._load_libs, tinyarray, chimerax.atomic.cymol, chimerax.atomic.cytmpl, chimerax.map._map, charset_normalizer.md, requests.packages.charset_normalizer.md, requests.packages.chardet.md, PIL._imaging, kiwisolver._cext, OpenGL_accelerate.errorchecker, OpenGL_accelerate.wrapper, OpenGL_accelerate.formathandler, OpenGL_accelerate.arraydatatype, OpenGL_accelerate.latebind, OpenGL_accelerate.vbo, chimerax.pdb_lib._load_libs, chimerax.surface._surface, chimerax.core._mac_util, OpenGL_accelerate.numpy_formathandler, OpenGL_accelerate.nones_formathandler, lz4._version, lz4.frame._frame, msgpack._cmsgpack, chimerax.core._serialize, PyQt6.QtOpenGL, PyQt6.QtOpenGLWidgets, chimerax.atomic._ribbons, chimerax.graphics._graphics, chimerax.mmcif._mmcif, chimerax.mmcif.mmcif, chimerax.pdb._pdbio, lxml._elementpath, lxml.etree, chimerax.atom_search.ast, chimerax.chem_group._chem_group, PIL._imagingmath, chimerax.alignment_algs._sw, chimerax.dssp._dssp, chimerax.alignment_algs._nw (total: 63)
{"app_name":"ChimeraX","timestamp":"2025-03-19 13:13:25.00 +0100","app_version":"1.9.0","slice_uuid":"17982d98-65bc-3327-8526-577ec996453c","build_version":"1.9.0.0","platform":1,"bundleID":"edu.ucsf.cgl.ChimeraX","share_with_app_devs":0,"is_first_party":0,"bug_type":"309","os_version":"macOS 14.6.1 (23G93)","roots_installed":0,"name":"ChimeraX","incident_id":"F133D96A-5022-4BEA-8BCF-F3089C81075E"}
{
"uptime" : 15000,
"procRole" : "Foreground",
"version" : 2,
"userID" : 501,
"deployVersion" : 210,
"modelCode" : "Mac14,9",
"coalitionID" : 1610,
"osVersion" : {
"train" : "macOS 14.6.1",
"build" : "23G93",
"releaseType" : "User"
},
"captureTime" : "2025-03-19 13:13:01.5478 +0100",
"codeSigningMonitor" : 1,
"incident" : "F133D96A-5022-4BEA-8BCF-F3089C81075E",
"pid" : 1607,
"translated" : false,
"cpuType" : "ARM-64",
"roots_installed" : 0,
"bug_type" : "309",
"procLaunch" : "2025-03-19 09:15:19.3595 +0100",
"procStartAbsTime" : 24155123195,
"procExitAbsTime" : 366442060614,
"procName" : "ChimeraX",
"procPath" : "\/Applications\/ChimeraX-1.9.app\/Contents\/MacOS\/ChimeraX",
"bundleInfo" : {"CFBundleShortVersionString":"1.9.0","CFBundleVersion":"1.9.0.0","CFBundleIdentifier":"edu.ucsf.cgl.ChimeraX"},
"storeInfo" : {"deviceIdentifierForVendor":"C5B03F29-781E-5981-B62A-D9CB0762ED5F","thirdParty":true},
"parentProc" : "launchd",
"parentPid" : 1,
"coalitionName" : "edu.ucsf.cgl.ChimeraX",
"crashReporterKey" : "CB4E980A-0873-E1D5-EDCE-43B1A3755214",
"codeSigningID" : "edu.ucsf.cgl.ChimeraX",
"codeSigningTeamID" : "LWV8X224YF",
"codeSigningFlags" : 570491649,
"codeSigningValidationCategory" : 6,
"codeSigningTrustLevel" : 4294967295,
"instructionByteStream" : {"beforePC":"fyMD1f17v6n9AwCRd+D\/l78DAJH9e8Go\/w9f1sADX9YQKYDSARAA1A==","atPC":"AwEAVH8jA9X9e7+p\/QMAkWzg\/5e\/AwCR\/XvBqP8PX9bAA1\/WcAqA0g=="},
"sleepWakeUUID" : "3120983D-03FA-44E9-BBF1-4FAF96DFBCAB",
"sip" : "enabled",
"vmRegionInfo" : "0x23fa6bdc2e18 is not in any region. Bytes after previous region: 39077422050841 Bytes before following region: 65994657878504\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"exception" : {"codes":"0x0000000000000001, 0x0000a3fa6bdc2e18","rawCodes":[1,180295946743320],"type":"EXC_BAD_ACCESS","signal":"SIGSEGV","subtype":"KERN_INVALID_ADDRESS at 0x0000a3fa6bdc2e18 -> 0x000023fa6bdc2e18 (possible pointer authentication failure)"},
"termination" : {"flags":0,"code":11,"namespace":"SIGNAL","indicator":"Segmentation fault: 11","byProc":"ChimeraX","byPid":1607},
"vmregioninfo" : "0x23fa6bdc2e18 is not in any region. Bytes after previous region: 39077422050841 Bytes before following region: 65994657878504\n REGION TYPE START - END [ VSIZE] PRT\/MAX SHRMOD REGION DETAIL\n commpage (reserved) 1000000000-7000000000 [384.0G] ---\/--- SM=NUL reserved VM address space (unallocated)\n---> GAP OF 0x5f9000000000 BYTES\n MALLOC_NANO 600000000000-600020000000 [512.0M] rw-\/rwx SM=PRV ",
"extMods" : {"caller":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"system":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"targeted":{"thread_create":0,"thread_set_state":0,"task_for_pid":0},"warnings":0},
"faultingThread" : 0,
"threads" : 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===== Log before crash start =====
Startup Messages
---
note | available bundle cache has not been initialized yet
You can double click a model's Name or ID in the model panel to edit those
fields
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
> open
> /Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen_DQH_base.cxs
opened ChimeraX session
> select #1
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show Contacts
> contacts sel ignoreHiddenModels true log true
Allowed overlap: -0.4
H-bond overlap reduction: 0.4
Ignore contacts between atoms separated by 4 bonds or less
Detect intra-residue contacts: False
Detect intra-molecule contacts: True
34 contacts
atom1 atom2 overlap distance
DQH #1/A DQH 402 O27 8fen #2/A THR 143 OG1 0.281 2.279
DQH #1/A DQH 402 C5 8fen #2/A LEU 207 CD1 0.265 3.195
DQH #1/A DQH 402 O23 8fen #2/A ASN 148 OD1 0.257 2.283
DQH #1/A DQH 402 O27 8fen #2/A THR 143 HG1 0.201 1.859
DQH #1/A DQH 402 O13 8fen #2/A THR 143 OG1 0.174 2.346
DQH #1/A DQH 402 C10 8fen #2/A THR 143 OG1 0.172 3.208
DQH #1/A DQH 402 C10 8fen #2/A THR 143 HG1 0.148 2.732
DQH #1/A DQH 402 O23 8fen #2/A ASN 148 CG 0.078 3.082
DQH #1/A DQH 402 C16 8fen #2/A GLN 242 OE1 0.046 3.194
DQH #1/A DQH 402 C9 8fen #2/A THR 143 OG1 0.044 3.066
DQH #1/A DQH 402 O13 8fen #2/A THR 143 HG1 0.042 1.978
DQH #1/A DQH 402 O13 8fen #2/A TYR 178 HH 0.010 2.010
DQH #1/A DQH 402 C9 8fen #2/A THR 143 HG1 -0.040 2.650
DQH #1/A DQH 402 O24 8fen #2/A GLN 242 OE1 -0.082 2.622
DQH #1/A DQH 402 O24 8fen #2/A ASN 148 HD21 -0.115 2.175
DQH #1/A DQH 402 O27 8fen #2/A ALA 144 H -0.123 2.183
DQH #1/A DQH 402 O27 8fen #2/A ALA 144 N -0.127 2.812
DQH #1/A DQH 402 O27 8fen #2/A ALA 144 HB3 -0.130 2.590
DQH #1/A DQH 402 C4 8fen #2/A LEU 207 CD1 -0.154 3.464
DQH #1/A DQH 402 O24 8fen #2/A ASN 148 ND2 -0.157 2.842
DQH #1/A DQH 402 O27 8fen #2/A ALA 144 CB -0.159 3.319
DQH #1/A DQH 402 C5 8fen #2/A LEU 207 HD12 -0.194 2.954
DQH #1/A DQH 402 O13 8fen #2/A TYR 178 OH -0.216 2.736
DQH #1/A DQH 402 C5 8fen #2/A LEU 207 HD13 -0.229 2.989
DQH #1/A DQH 402 C17 8fen #2/A GLN 242 OE1 -0.233 3.323
DQH #1/A DQH 402 O13 8fen #2/A THR 143 CB -0.241 3.361
DQH #1/A DQH 402 C19 8fen #2/A ALA 144 HB3 -0.287 3.047
DQH #1/A DQH 402 O27 8fen #2/A ALA 144 CA -0.298 3.458
DQH #1/A DQH 402 C18 8fen #2/A ASN 148 OD1 -0.309 3.399
DQH #1/A DQH 402 C19 8fen #2/A GLY 145 N -0.356 3.741
DQH #1/A DQH 402 C5 8fen #2/A LEU 207 HD11 -0.363 3.123
DQH #1/A DQH 402 C4 8fen #2/A LEU 207 HD12 -0.372 2.982
DQH #1/A DQH 402 C15 8fen #2/A ALA 144 HB3 -0.375 3.135
DQH #1/A DQH 402 O24 8fen #2/A GLN 242 CD -0.390 3.550
34 contacts
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
2 8fen
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A DQH 402 O24 8fen #2/A GLN 242 OE1 no hydrogen 2.622 N/A
DQH #1/A DQH 402 O27 8fen #2/A THR 143 OG1 no hydrogen 2.279 N/A
DQH #1/A DQH 402 O27 8fen #2/A PRO 205 O no hydrogen 3.495 N/A
DQH #1/A DQH 402 O30 DQH #1/A DQH 402 O13 no hydrogen 2.654 N/A
DQH #1/A DQH 402 O30 8fen #2/A TYR 178 OH no hydrogen 3.163 N/A
8fen #2/A ALA 144 N DQH #1/A DQH 402 O27 8fen #2/A ALA 144 H 2.812 2.183
8fen #2/A ASN 148 ND2 DQH #1/A DQH 402 O24 8fen #2/A ASN 148 HD21 2.842 2.175
8fen #2/A TYR 178 OH DQH #1/A DQH 402 O13 8fen #2/A TYR 178 HH 2.736 2.010
8 hydrogen bonds found
> close #4.1
> close #3-4
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
2 8fen
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A DQH 402 O24 8fen #2/A GLN 242 OE1 no hydrogen 2.622 N/A
DQH #1/A DQH 402 O27 8fen #2/A THR 143 OG1 no hydrogen 2.279 N/A
DQH #1/A DQH 402 O27 8fen #2/A PRO 205 O no hydrogen 3.495 N/A
DQH #1/A DQH 402 O30 DQH #1/A DQH 402 O13 no hydrogen 2.654 N/A
DQH #1/A DQH 402 O30 8fen #2/A TYR 178 OH no hydrogen 3.163 N/A
8fen #2/A ALA 144 N DQH #1/A DQH 402 O27 8fen #2/A ALA 144 H 2.812 2.183
8fen #2/A ASN 148 ND2 DQH #1/A DQH 402 O24 8fen #2/A ASN 148 HD21 2.842 2.175
8fen #2/A TYR 178 OH DQH #1/A DQH 402 O13 8fen #2/A TYR 178 HH 2.736 2.010
8 hydrogen bonds found
> close #3.1
> view matrix camera
> 0.61601,0.61631,-0.49061,16.229,0.423,-0.78419,-0.454,-5.2541,-0.66454,0.07214,-0.74377,-40.779
> swapaa interactive #2:148 Cys
8fen #2/A ASN 148: phi -117.1, psi 19.0 trans
Changed 9 bond radii
> select #2:148
14 atoms, 13 bonds, 1 residue, 1 model selected
> ~label (#!2 & sel) residues
> close session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250212_8FEN_DHM_A1model3.cxs"
opened ChimeraX session
> ui tool show "Side View"
> hide sel surfaces
> view matrix camera
> 0.61601,0.61631,-0.49061,16.229,0.423,-0.78419,-0.454,-5.2541,-0.66454,0.07214,-0.74377,-40.779
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Showing
> effect of H bonds/8fen_DQH_base.cxs"
opened ChimeraX session
> addh #1
Summary of feedback from adding hydrogens to DQH #1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
1 hydrogen bonds
12 hydrogens added
> close session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Showing
> effect of H bonds/8fen_DQH_base.cxs"
opened ChimeraX session
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
2 8fen
8 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A DQH 402 O24 8fen #2/A GLN 242 OE1 no hydrogen 2.622 N/A
DQH #1/A DQH 402 O27 8fen #2/A THR 143 OG1 no hydrogen 2.279 N/A
DQH #1/A DQH 402 O27 8fen #2/A PRO 205 O no hydrogen 3.495 N/A
DQH #1/A DQH 402 O30 DQH #1/A DQH 402 O13 no hydrogen 2.654 N/A
DQH #1/A DQH 402 O30 8fen #2/A TYR 178 OH no hydrogen 3.163 N/A
8fen #2/A ALA 144 N DQH #1/A DQH 402 O27 8fen #2/A ALA 144 H 2.812 2.183
8fen #2/A ASN 148 ND2 DQH #1/A DQH 402 O24 8fen #2/A ASN 148 HD21 2.842 2.175
8fen #2/A TYR 178 OH DQH #1/A DQH 402 O13 8fen #2/A TYR 178 HH 2.736 2.010
8 hydrogen bonds found
> close #3
> addh #1
Summary of feedback from adding hydrogens to DQH #1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
1 hydrogen bonds
12 hydrogens added
> select #1
34 atoms, 36 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
2 8fen
6 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A DQH 402 O27 8fen #2/A PRO 205 O DQH #1/A DQH 402 H27 3.495 2.759
DQH #1/A DQH 402 O30 DQH #1/A DQH 402 O13 DQH #1/A DQH 402 H30 2.654 1.880
DQH #1/A DQH 402 O30 8fen #2/A TYR 178 OH DQH #1/A DQH 402 H30 3.163 2.352
8fen #2/A ALA 144 N DQH #1/A DQH 402 O27 8fen #2/A ALA 144 H 2.812 2.183
8fen #2/A ASN 148 ND2 DQH #1/A DQH 402 O24 8fen #2/A ASN 148 HD21 2.842 2.175
8fen #2/A TYR 178 OH DQH #1/A DQH 402 O13 8fen #2/A TYR 178 HH 2.736 2.010
6 hydrogen bonds found
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQH_base.cxs"
opened ChimeraX session
> open
> /Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/A1-AlphaFold_Heidi_A1_repeat_1a660/Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#3
---
Chain | Description
A | No description available
Computing secondary structure
> rename #3 A1
> matchmaker #3 to #1
No matrix compatible with both reference structure and all match structures
> matchmaker #3 to #2
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8fen, chain A (#2) with A1, chain A (#3), sequence alignment score
= 1522.3
RMSD between 307 pruned atom pairs is 0.625 angstroms; (across all 325 pairs:
1.244)
> close #2
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1.cxs"
> select #138
Nothing selected
> select #2:138
Nothing selected
> select #3:138
8 atoms, 7 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1.cxs"
> swapaa interactive #3:138 Cys
A1 #3/A ASN 138: phi -130.5, psi 2.4 trans
Changed 9 bond radii
> swapaa #!3/A:138 Cys criteria 1 rotLib Dunbrack
Using Dunbrack library
A1 #!3/A ASN 138: phi -130.5, psi 2.4 trans
Applying CYS rotamer (chi angles: -61.9) to A1 #!3/A CYS 138
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
3 A1
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A DQH 402 O24 A1 #3/A GLN 232 OE1 no hydrogen 2.563 N/A
DQH #1/A DQH 402 O27 A1 #3/A SER 133 OG no hydrogen 2.619 N/A
DQH #1/A DQH 402 O29 A1 #3/A THR 213 OG1 no hydrogen 2.989 N/A
DQH #1/A DQH 402 O30 DQH #1/A DQH 402 O13 no hydrogen 2.654 N/A
DQH #1/A DQH 402 O30 A1 #3/A TYR 168 OH no hydrogen 3.188 N/A
A1 #3/A SER 133 OG DQH #1/A DQH 402 O13 no hydrogen 2.808 N/A
A1 #3/A SER 133 OG DQH #1/A DQH 402 O27 no hydrogen 2.619 N/A
A1 #3/A GLY 135 N DQH #1/A DQH 402 O27 no hydrogen 3.284 N/A
A1 #3/A TYR 168 OH DQH #1/A DQH 402 O13 no hydrogen 2.883 N/A
A1 #3/A THR 213 OG1 DQH #1/A DQH 402 O29 no hydrogen 2.989 N/A
10 hydrogen bonds found
> close session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1.cxs" format session
opened ChimeraX session
> swapaa interactive #3:138 Cys
A1 #3/A ASN 138: phi -130.5, psi 2.4 trans
Changed 9 bond radii
> hbonds #!3 & ~#!3/A:138 & ~solvent reveal true restrict #3.2 & ~@c,ca,n
0 hydrogen bonds found
> clashes #!3 & ~#!3/A:138 & ~solvent radius 0.075 reveal true restrict #3.2 &
> ~@c,ca,n
4 clashes
> hbonds #!3 & ~#!3/A:138 & ~solvent reveal true restrict #3.2 & ~@c,ca,n
0 hydrogen bonds found
> clashes #!3 & ~#!3/A:138 & ~solvent radius 0.075 reveal true restrict #3.2 &
> ~@c,ca,n
4 clashes
> swapaa #!3/A:138 Cys criteria 2 rotLib Dunbrack
Using Dunbrack library
A1 #!3/A ASN 138: phi -130.5, psi 2.4 trans
Applying CYS rotamer (chi angles: 66.3) to A1 #!3/A CYS 138
> select #1/A:402@C17
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> close #4
> close #2
> swapaa interactive #3:138 Cys
A1 #3/A CYS 138: phi -130.5, psi 2.4 trans
Changed 9 bond radii
> swapaa #!3/A:138 Cys criteria 2 rotLib Dunbrack
Using Dunbrack library
A1 #!3/A CYS 138: phi -130.5, psi 2.4 trans
Applying CYS rotamer (chi angles: 66.3) to A1 #!3/A CYS 138
> select #3:138
6 atoms, 5 bonds, 1 residue, 1 model selected
> show sel atoms
> ~label sel residues
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #3/A:147@OH
1 atom, 1 residue, 1 model selected
> select up
12 atoms, 12 bonds, 1 residue, 1 model selected
> hide sel atoms
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1mut.cxs"
> close session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQH_base.cxs"
opened ChimeraX session
> open
> /Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/A1*-AlphaFold_test_30028_A1*/test_30028_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
test_30028_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> rename #3 to A1*
Expected a keyword
> rename #3 to A1star
Expected a keyword
> rename #3 A1*
> matchmaker #3 to #
Invalid "to" argument: invalid atoms specifier
> matchmaker #3 to #2
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8fen, chain A (#2) with A1*, chain A (#3), sequence alignment score
= 1542.4
RMSD between 312 pruned atom pairs is 0.596 angstroms; (across all 325 pairs:
0.914)
> close #2
> select #3:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #3:136
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> select #3:138
9 atoms, 8 bonds, 1 residue, 1 model selected
> ~label sel residues
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1*.cxs"
> swapaa interactive #3:136 Asn
A1* #3/A CYS 136: phi -129.7, psi 3.1 trans
Changed 180 bond radii
No rotamers selected. Click the 'Calculate' button (not 'OK') to add a column
to the table.
> swapaa #!3/A:136 Asn criteria
> 1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,32,33,34,35,36
> rotLib Dunbrack
Using Dunbrack library
A1* #!3/A CYS 136: phi -129.7, psi 3.1 trans
Applying ASN rotamer (chi angles: 62.9 6.5) to A1* #!3/A ASN 136 using alt loc
A
Applying ASN rotamer (chi angles: -66.2 -64.3) to A1* #!3/A ASN 136 using alt
loc B
Applying ASN rotamer (chi angles: 62.9 34.7) to A1* #!3/A ASN 136 using alt
loc C
Applying ASN rotamer (chi angles: 62.9 -21.7) to A1* #!3/A ASN 136 using alt
loc D
Applying ASN rotamer (chi angles: -66.2 -36.5) to A1* #!3/A ASN 136 using alt
loc E
Applying ASN rotamer (chi angles: -66.2 -90.0) to A1* #!3/A ASN 136 using alt
loc F
Applying ASN rotamer (chi angles: 62.9 -50.3) to A1* #!3/A ASN 136 using alt
loc G
Applying ASN rotamer (chi angles: 62.9 63.1) to A1* #!3/A ASN 136 using alt
loc H
Applying ASN rotamer (chi angles: -66.2 -9.0) to A1* #!3/A ASN 136 using alt
loc I
Applying ASN rotamer (chi angles: -66.2 115.3) to A1* #!3/A ASN 136 using alt
loc J
Applying ASN rotamer (chi angles: -163.1 38.6) to A1* #!3/A ASN 136 using alt
loc K
Applying ASN rotamer (chi angles: -66.2 87.6) to A1* #!3/A ASN 136 using alt
loc L
Applying ASN rotamer (chi angles: -66.2 142.5) to A1* #!3/A ASN 136 using alt
loc M
Applying ASN rotamer (chi angles: 62.9 -79.2) to A1* #!3/A ASN 136 using alt
loc N
Applying ASN rotamer (chi angles: 62.9 92.2) to A1* #!3/A ASN 136 using alt
loc O
Applying ASN rotamer (chi angles: -163.1 65.5) to A1* #!3/A ASN 136 using alt
loc P
Applying ASN rotamer (chi angles: -163.1 11.8) to A1* #!3/A ASN 136 using alt
loc Q
Applying ASN rotamer (chi angles: -66.2 23.1) to A1* #!3/A ASN 136 using alt
loc R
Applying ASN rotamer (chi angles: -66.2 57.6) to A1* #!3/A ASN 136 using alt
loc S
Applying ASN rotamer (chi angles: -66.2 -117.2) to A1* #!3/A ASN 136 using alt
loc T
Applying ASN rotamer (chi angles: -66.2 171.0) to A1* #!3/A ASN 136 using alt
loc U
Applying ASN rotamer (chi angles: -163.1 94.1) to A1* #!3/A ASN 136 using alt
loc V
Applying ASN rotamer (chi angles: 62.9 -109.5) to A1* #!3/A ASN 136 using alt
loc W
Applying ASN rotamer (chi angles: -163.1 -17.0) to A1* #!3/A ASN 136 using alt
loc X
Applying ASN rotamer (chi angles: 62.9 122.3) to A1* #!3/A ASN 136 using alt
loc Y
Applying ASN rotamer (chi angles: -163.1 -111.7) to A1* #!3/A ASN 136 using
alt loc Z
Applying ASN rotamer (chi angles: -163.1 -140.1) to A1* #!3/A ASN 136 using
alt loc a
Applying ASN rotamer (chi angles: -163.1 -83.3) to A1* #!3/A ASN 136 using alt
loc b
Applying ASN rotamer (chi angles: -66.2 -155.4) to A1* #!3/A ASN 136 using alt
loc c
Applying ASN rotamer (chi angles: 62.9 -141.9) to A1* #!3/A ASN 136 using alt
loc d
Applying ASN rotamer (chi angles: -163.1 -51.4) to A1* #!3/A ASN 136 using alt
loc e
Applying ASN rotamer (chi angles: -163.1 -169.1) to A1* #!3/A ASN 136 using
alt loc f
Applying ASN rotamer (chi angles: 62.9 155.0) to A1* #!3/A ASN 136 using alt
loc g
Applying ASN rotamer (chi angles: 62.9 -173.1) to A1* #!3/A ASN 136 using alt
loc h
Applying ASN rotamer (chi angles: -163.1 124.9) to A1* #!3/A ASN 136 using alt
loc i
Applying ASN rotamer (chi angles: -163.1 159.7) to A1* #!3/A ASN 136 using alt
loc j
> swapaa interactive #3:136 Asn
A1* #3/A ASN 136: phi -129.7, psi 3.1 trans
Changed 180 bond radii
> clashes #!3 & ~#!3/A:136 & ~solvent radius 0.075 reveal true restrict #3.2 &
> ~@c,ca,n
145 clashes
> swapaa #!3/A:136 Asn criteria 1 rotLib Dunbrack
Using Dunbrack library
A1* #!3/A ASN 136: phi -129.7, psi 3.1 trans
Applying ASN rotamer (chi angles: 62.9 6.5) to A1* #!3/A ASN 136
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> close #2
> rename #3 A1*mut
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1*mut.cxs"
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
3 A1*mut
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A DQH 402 O24 A1*mut #3/A GLN 230 OE1 no hydrogen 2.968 N/A
DQH #1/A DQH 402 O27 A1*mut #3/A SER 131 OG no hydrogen 2.492 N/A
DQH #1/A DQH 402 O29 A1*mut #3/A THR 211 OG1 no hydrogen 2.856 N/A
DQH #1/A DQH 402 O30 DQH #1/A DQH 402 O13 no hydrogen 2.654 N/A
DQH #1/A DQH 402 O30 A1*mut #3/A TYR 166 OH no hydrogen 3.239 N/A
A1*mut #3/A SER 131 OG DQH #1/A DQH 402 O13 no hydrogen 2.787 N/A
A1*mut #3/A SER 131 OG DQH #1/A DQH 402 O27 no hydrogen 2.492 N/A
A1*mut #3/A GLY 133 N DQH #1/A DQH 402 O27 no hydrogen 3.339 N/A
A1*mut #3/A TYR 166 OH DQH #1/A DQH 402 O13 no hydrogen 2.862 N/A
A1*mut #3/A THR 211 OG1 DQH #1/A DQH 402 O29 no hydrogen 2.856 N/A
10 hydrogen bonds found
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1*mut_Hbondds.cxs"
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1*.cxs"
opened ChimeraX session
> select #1/A:402@C19
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> select up
2723 atoms, 2784 bonds, 354 residues, 2 models selected
> select down
22 atoms, 24 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
3 A1*
12 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A DQH 402 O24 A1* #3/A GLN 230 OE1 no hydrogen 2.968 N/A
DQH #1/A DQH 402 O27 A1* #3/A SER 131 OG no hydrogen 2.492 N/A
DQH #1/A DQH 402 O29 A1* #3/A THR 211 OG1 no hydrogen 2.856 N/A
DQH #1/A DQH 402 O30 DQH #1/A DQH 402 O13 no hydrogen 2.654 N/A
DQH #1/A DQH 402 O30 A1* #3/A TYR 166 OH no hydrogen 3.239 N/A
A1* #3/A SER 131 OG DQH #1/A DQH 402 O13 no hydrogen 2.787 N/A
A1* #3/A SER 131 OG DQH #1/A DQH 402 O27 no hydrogen 2.492 N/A
A1* #3/A GLY 133 N DQH #1/A DQH 402 O27 no hydrogen 3.339 N/A
A1* #3/A CYS 136 SG DQH #1/A DQH 402 O23 no hydrogen 2.289 N/A
A1* #3/A CYS 136 SG DQH #1/A DQH 402 O24 no hydrogen 3.105 N/A
A1* #3/A TYR 166 OH DQH #1/A DQH 402 O13 no hydrogen 2.862 N/A
A1* #3/A THR 211 OG1 DQH #1/A DQH 402 O29 no hydrogen 2.856 N/A
12 hydrogen bonds found
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1*_Hbonds.cxs"
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1.cxs"
opened ChimeraX session
> select #1/A:402@O23
1 atom, 1 residue, 1 model selected
> ui tool show "Change Chain IDs"
> ui tool show "Build Structure"
> build modify #1/A:402@O23 O 2 geometry tetrahedral resName UNL
> close session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1.cxs"
opened ChimeraX session
> select #1/A:402@O23
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build modify #1/A:402@O23 H 1 name H1 resName UNL
> ui tool show "Build Structure"
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHK_A1.cxs"
> swapaa interactive #3:138 Cys
A1 #3/A ASN 138: phi -130.5, psi 2.4 trans
Changed 9 bond radii
> swapaa #!3/A:138 Cys criteria 2 rotLib Dunbrack
Using Dunbrack library
A1 #!3/A ASN 138: phi -130.5, psi 2.4 trans
Applying CYS rotamer (chi angles: 66.3) to A1 #!3/A CYS 138
> select #3:138
6 atoms, 5 bonds, 1 residue, 1 model selected
> ~label sel residues
> label sel text "{0.name} {0.number}{0.insertion_code}"
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHK_A1mut.cxs"
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHQ_A1*.cxs"
opened ChimeraX session
> select #1/A:402@O23
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build modify #1/A:402@O23 H 1 name H1 resName UNL
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHK_A1*.cxs"
> swapaa interactive #3:136 Asn
A1* #3/A CYS 136: phi -129.7, psi 3.1 trans
Changed 180 bond radii
> swapaa #!3/A:136 Asn criteria 1 rotLib Dunbrack
Using Dunbrack library
A1* #!3/A CYS 136: phi -129.7, psi 3.1 trans
Applying ASN rotamer (chi angles: 62.9 6.5) to A1* #!3/A ASN 136
> select #3:136
8 atoms, 7 bonds, 1 residue, 1 model selected
> ~label sel residues
> label sel text "{0.name} {0.number}{0.insertion_code}"
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHK_A1*mut.cxs"
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best
> model)/DHM_manualdock/250212_8FEN_DHM_finalmanualdock.cxs"
opened ChimeraX session
> rename #2 DHM
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Showing
> effect of H bonds/8fen_DHQ_DHMmanualdock.cxs"
> close #1
> select #2/?:1@C6
1 atom, 1 residue, 1 model selected
> select up
35 atoms, 37 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 DHM
3 Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DHM #2/? UNL 1 O4 DHM #2/? UNL 1 O3 DHM #2/? UNL 1 H8 2.598 1.776
DHM #2/? UNL 1 O5 Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A GLN 232 OE1 DHM #2/? UNL 1 H9 3.020 2.156
DHM #2/? UNL 1 O7 Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A THR 213 OG1 DHM #2/? UNL 1 H11 2.824 2.054
Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A SER 133 OG DHM #2/? UNL 1 O2 no hydrogen 2.497 N/A
Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A SER 133 OG DHM #2/? UNL 1 O3 no hydrogen 3.072 N/A
Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A GLY 135 N DHM #2/? UNL 1 O2 no hydrogen 3.218 N/A
Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A TYR 168 OH DHM #2/? UNL 1 O3 no hydrogen 3.037 N/A
Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A THR 213 OG1 DHM #2/? UNL 1 O7 no hydrogen 2.824 N/A
Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3/A GLN 232 N DHM #2/? UNL 1 O5 no hydrogen 3.217 N/A
9 hydrogen bonds found
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best
> model)/DHM_manualdock/250212_8FEN_DHM_manualdock_torsion.cxs"
opened ChimeraX session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best
> model)/DHM_manualdock/250212_8FEN_DHM_finalmanualdock.cxs"
opened ChimeraX session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Showing
> effect of H bonds/8fen_DHQ_DHMmanualdock.cxs"
opened ChimeraX session
> close #1
> rename #3 A1
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
35 atoms, 37 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 DHM
3 A1
9 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DHM #2/? UNL 1 O4 DHM #2/? UNL 1 O3 DHM #2/? UNL 1 H8 2.598 1.776
DHM #2/? UNL 1 O5 A1 #3/A GLN 232 OE1 DHM #2/? UNL 1 H9 3.020 2.156
DHM #2/? UNL 1 O7 A1 #3/A THR 213 OG1 DHM #2/? UNL 1 H11 2.824 2.054
A1 #3/A SER 133 OG DHM #2/? UNL 1 O2 no hydrogen 2.497 N/A
A1 #3/A SER 133 OG DHM #2/? UNL 1 O3 no hydrogen 3.072 N/A
A1 #3/A GLY 135 N DHM #2/? UNL 1 O2 no hydrogen 3.218 N/A
A1 #3/A TYR 168 OH DHM #2/? UNL 1 O3 no hydrogen 3.037 N/A
A1 #3/A THR 213 OG1 DHM #2/? UNL 1 O7 no hydrogen 2.824 N/A
A1 #3/A GLN 232 N DHM #2/? UNL 1 O5 no hydrogen 3.217 N/A
9 hydrogen bonds found
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Showing
> effect of H bonds/8fen_DHQ_DHMmanualdock_Hbonds.cxs"
> ui mousemode right "move picked models"
> ui mousemode right "translate selected atoms"
> ui mousemode right "rotate selected models"
> view matrix models
> #2,0.78526,-0.3061,0.53821,51.035,-0.32322,-0.94407,-0.065337,26.485,0.5281,-0.12265,-0.84028,9.4542
> close #1
> view matrix models
> #2,0.76165,-0.30442,0.57203,50.969,-0.37399,-0.92742,0.004406,26.349,0.52918,-0.21729,-0.82022,9.4166
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
2 DHM
3 A1
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DHM #2/? UNL 1 O4 DHM #2/? UNL 1 O3 DHM #2/? UNL 1 H8 2.598 1.776
DHM #2/? UNL 1 O4 A1 #3/A TYR 168 OH DHM #2/? UNL 1 H8 3.254 2.506
DHM #2/? UNL 1 O5 A1 #3/A GLN 232 OE1 DHM #2/? UNL 1 H9 3.034 2.117
DHM #2/? UNL 1 O7 A1 #3/A THR 213 OG1 DHM #2/? UNL 1 H11 2.800 2.013
A1 #3/A SER 133 OG DHM #2/? UNL 1 O2 no hydrogen 2.335 N/A
A1 #3/A SER 133 OG DHM #2/? UNL 1 O3 no hydrogen 2.832 N/A
A1 #3/A GLY 135 N DHM #2/? UNL 1 O2 no hydrogen 2.989 N/A
A1 #3/A TYR 168 OH DHM #2/? UNL 1 O3 no hydrogen 2.772 N/A
A1 #3/A THR 213 OG1 DHM #2/? UNL 1 O7 no hydrogen 2.800 N/A
A1 #3/A GLN 232 N DHM #2/? UNL 1 O5 no hydrogen 3.195 N/A
10 hydrogen bonds found
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Showing
> effect of H bonds/8fen_DHQ_DHMmanualdockrot_Hbonds.cxs"
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQH_base.cxs"
opened ChimeraX session
> select #1/A:402@C16
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> select #1/A:402@C17
1 atom, 1 residue, 1 model selected
> select up
22 atoms, 24 bonds, 1 residue, 1 model selected
> addh #1
Summary of feedback from adding hydrogens to DQH #1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
1 hydrogen bonds
12 hydrogens added
> select #1/A:402@H16
1 atom, 1 residue, 1 model selected
> build modify #1/A:402@H16 O 2 geometry linear name O1 resName UNL
> select #1/A:402@H23
1 atom, 1 residue, 1 model selected
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMlinearbond.cxs"
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHM_Hbonds.cxs"
opened ChimeraX session
> view matrix models
> #2,0.98629,0.083579,-0.14227,0.70391,-0.079822,0.9963,0.031922,4.0815,0.14442,-0.020128,0.98931,-7.3854
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQH_base.cxs"
opened ChimeraX session
> select #1/A:402@C16
1 atom, 1 residue, 1 model selected
> ui tool show "Selection Inspector"
> addh #1
Summary of feedback from adding hydrogens to DQH #1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
1 hydrogen bonds
12 hydrogens added
> select #1/A:402@H16
1 atom, 1 residue, 1 model selected
> ui mousemode right translate
> close session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQH_base.cxs"
opened ChimeraX session
> addh #1
Summary of feedback from adding hydrogens to DQH #1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
1 hydrogen bonds
12 hydrogens added
> select #1/A:402@H16
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build modify #1/A:402@H16 O 2 geometry trigonal name O1 resName UNL
> build modify #1/A:402@O1 O 2 geometry trigonal
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMtrigonalbond.cxs"
> select up
35 atoms, 37 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
2 8fen
7 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A UNL 402 O27 8fen #2/A PRO 205 O DQH #1/A UNL 402 H27 3.495 2.759
DQH #1/A UNL 402 O30 DQH #1/A UNL 402 O13 DQH #1/A UNL 402 H30 2.654 1.880
DQH #1/A UNL 402 O30 8fen #2/A TYR 178 OH DQH #1/A UNL 402 H30 3.163 2.352
8fen #2/A ALA 144 N DQH #1/A UNL 402 O27 8fen #2/A ALA 144 H 2.812 2.183
8fen #2/A ASN 148 ND2 DQH #1/A UNL 402 O24 8fen #2/A ASN 148 HD21 2.842 2.175
8fen #2/A TYR 178 OH DQH #1/A UNL 402 O13 8fen #2/A TYR 178 HH 2.736 2.010
8fen #2/A GLN 242 N DQH #1/A UNL 402 O1 8fen #2/A GLN 242 H 3.232 2.398
7 hydrogen bonds found
> select #2:143
14 atoms, 13 bonds, 1 residue, 1 model selected
> show sel atoms
> close #3
> select #1/A:402@H11
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A:174@CG2
1 atom, 1 residue, 1 model selected
> select #1/A:402@H30
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H1
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H29
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H5
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H15
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H2
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H23
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H19
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H10
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H24
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H27
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMtrigonalbond_Hdeleted.cxs"
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
2 8fen
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A UNL 402 O1 8fen #2/A GLN 242 OE1 no hydrogen 2.328 N/A
DQH #1/A UNL 402 O24 8fen #2/A GLN 242 OE1 no hydrogen 2.622 N/A
DQH #1/A UNL 402 O27 8fen #2/A THR 143 OG1 no hydrogen 2.279 N/A
DQH #1/A UNL 402 O27 8fen #2/A PRO 205 O no hydrogen 3.495 N/A
DQH #1/A UNL 402 O30 DQH #1/A UNL 402 O13 no hydrogen 2.654 N/A
DQH #1/A UNL 402 O30 8fen #2/A TYR 178 OH no hydrogen 3.163 N/A
8fen #2/A ALA 144 N DQH #1/A UNL 402 O27 8fen #2/A ALA 144 H 2.812 2.183
8fen #2/A ASN 148 ND2 DQH #1/A UNL 402 O24 8fen #2/A ASN 148 HD21 2.842 2.175
8fen #2/A TYR 178 OH DQH #1/A UNL 402 O13 8fen #2/A TYR 178 HH 2.736 2.010
8fen #2/A GLN 242 N DQH #1/A UNL 402 O1 8fen #2/A GLN 242 H 3.232 2.398
10 hydrogen bonds found
> close session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQH_base.cxs" format session
opened ChimeraX session
> select #1/A:402@C16
1 atom, 1 residue, 1 model selected
> addh #1
Summary of feedback from adding hydrogens to DQH #1
---
notes | Chain-initial residues that are actual N termini:
Chain-initial residues that are not actual N termini:
Chain-final residues that are actual C termini:
Chain-final residues that are not actual C termini:
1 hydrogen bonds
12 hydrogens added
> select #1/A:402@H16
1 atom, 1 residue, 1 model selected
> ui tool show "Build Structure"
> build modify #1/A:402@H16 O 2 geometry tetrahedral name O1 resName UNL
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMtetrahedralbond.cxs"
> select #1/A:402@H19
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H23
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H2
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H15
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H10
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H11
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H30
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H5
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H29
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #2/A:32@HB
1 atom, 1 residue, 1 model selected
> select #1/A:402@H1
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H27
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H24
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMtetrahedralbond_Hdeleted.cxs"
> select #1/A:402@C11
1 atom, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> select up
4985 atoms, 5046 bonds, 327 residues, 2 models selected
> select down
23 atoms, 25 bonds, 1 residue, 2 models selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
2 8fen
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A UNL 402 O1 8fen #2/A GLN 242 OE1 no hydrogen 2.272 N/A
DQH #1/A UNL 402 O24 8fen #2/A GLN 242 OE1 no hydrogen 2.622 N/A
DQH #1/A UNL 402 O27 8fen #2/A THR 143 OG1 no hydrogen 2.279 N/A
DQH #1/A UNL 402 O27 8fen #2/A PRO 205 O no hydrogen 3.495 N/A
DQH #1/A UNL 402 O30 DQH #1/A UNL 402 O13 no hydrogen 2.654 N/A
DQH #1/A UNL 402 O30 8fen #2/A TYR 178 OH no hydrogen 3.163 N/A
8fen #2/A ALA 144 N DQH #1/A UNL 402 O27 8fen #2/A ALA 144 H 2.812 2.183
8fen #2/A ASN 148 ND2 DQH #1/A UNL 402 O24 8fen #2/A ASN 148 HD21 2.842 2.175
8fen #2/A TYR 178 OH DQH #1/A UNL 402 O13 8fen #2/A TYR 178 HH 2.736 2.010
8fen #2/A GLN 242 N DQH #1/A UNL 402 O1 8fen #2/A GLN 242 H 3.123 2.291
10 hydrogen bonds found
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMlinearbond.cxs"
opened ChimeraX session
> select #1/A:402@H15
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H19
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H23
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H29
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H2
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H11
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H30
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H1
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H5
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H27
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H10
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select #1/A:402@H24
1 atom, 1 residue, 1 model selected
> delete atoms sel
> delete bonds sel
> select up
2 atoms, 1 bond, 1 residue, 1 model selected
> select up
23 atoms, 25 bonds, 1 residue, 1 model selected
> ui tool show H-Bonds
> hbonds sel color #ff37fe dashes 6 showDist true reveal true retainCurrent
> true log true
Finding intermodel H-bonds
Finding intramodel H-bonds
Constraints relaxed by 0.4 angstroms and 20 degrees
Models used:
1 DQH
2 8fen
10 H-bonds
H-bonds (donor, acceptor, hydrogen, D..A dist, D-H..A dist):
DQH #1/A UNL 402 O1 8fen #2/A GLN 242 OE1 no hydrogen 2.328 N/A
DQH #1/A UNL 402 O24 8fen #2/A GLN 242 OE1 no hydrogen 2.622 N/A
DQH #1/A UNL 402 O27 8fen #2/A THR 143 OG1 no hydrogen 2.279 N/A
DQH #1/A UNL 402 O27 8fen #2/A PRO 205 O no hydrogen 3.495 N/A
DQH #1/A UNL 402 O30 DQH #1/A UNL 402 O13 no hydrogen 2.654 N/A
DQH #1/A UNL 402 O30 8fen #2/A TYR 178 OH no hydrogen 3.163 N/A
8fen #2/A ALA 144 N DQH #1/A UNL 402 O27 8fen #2/A ALA 144 H 2.812 2.183
8fen #2/A ASN 148 ND2 DQH #1/A UNL 402 O24 8fen #2/A ASN 148 HD21 2.842 2.175
8fen #2/A TYR 178 OH DQH #1/A UNL 402 O13 8fen #2/A TYR 178 HH 2.736 2.010
8fen #2/A GLN 242 N DQH #1/A UNL 402 O1 8fen #2/A GLN 242 H 3.232 2.398
10 hydrogen bonds found
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMlinearbond_Hdeleted.cxs"
> close #3
> open
> /Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/A1-AlphaFold_Heidi_A1_repeat_1a660/Heidi_A1_repeat_1a660_scores_rank_001_alphafold2_ptm_model_3_seed_000.json
Traceback (most recent call last):
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/dialog.py", line 334, in _qt_safe
run(session, "open " + " ".join([FileNameArg.unparse(p) for p in paths]) + (""
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/run.py", line 49, in run
results = command.run(text, log=log, return_json=return_json)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 132, in cmd_open
models = Command(session, registry=registry).run(provider_cmd_text,
log=log)[0]
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/core/commands/cli.py", line 3213, in run
result = ci.function(session, **kw_args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 215, in provider_open
models, status = collated_open(session, None, [data], data_format,
_add_models,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 526, in collated_open
return remember_data_format()
^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/open_command/cmd.py", line 497, in remember_data_format
models, status = func(*func_args, **func_kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/__init__.py", line 129, in open
pae = alphafold_pae(session, file = path, **kw)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1445, in alphafold_pae
structure = _guess_pae_associated_structure(session, file)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1504, in
_guess_pae_associated_structure
structs = [m for m in session.models.list(type = AtomicStructure)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File
"/Applications/ChimeraX-1.9.app/Contents/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-
packages/chimerax/alphafold/pae.py", line 1505, in
if hasattr(m, 'filename') and dirname(m.filename) == dirname(pae_path)]
^^^^^^^^^^^^^^^^^^^
File "", line 152, in dirname
TypeError: expected str, bytes or os.PathLike object, not NoneType
TypeError: expected str, bytes or os.PathLike object, not NoneType
File "", line 152, in dirname
See log for complete Python traceback.
> open
> /Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/A1-AlphaFold_Heidi_A1_repeat_1a660/Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
Heidi_A1_repeat_1a660_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
#3
---
Chain | Description
A | No description available
Computing secondary structure
> rename #3 A1
> matchmaker #3 to #2
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8fen, chain A (#2) with A1, chain A (#3), sequence alignment score
= 1522.3
RMSD between 307 pruned atom pairs is 0.625 angstroms; (across all 325 pairs:
1.244)
> rename #1 DHM
> close #2
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHM_A1.cxs"
> swapaa interactive #3:138 Cys
A1 #3/A ASN 138: phi -130.5, psi 2.4 trans
Changed 9 bond radii
> swapaa #!3/A:138 Cys criteria 2 rotLib Dunbrack
Using Dunbrack library
A1 #!3/A ASN 138: phi -130.5, psi 2.4 trans
Applying CYS rotamer (chi angles: 66.3) to A1 #!3/A CYS 138
> select #3:138
6 atoms, 5 bonds, 1 residue, 1 model selected
> label sel text "{0.name} {0.number}{0.insertion_code}"
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHM_A1mut.cxs"
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMlinearbond.cxs"
opened ChimeraX session
> open
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/8fen
> and substrates/8fen_DQHtoDHMlinearbond_Hdeleted.cxs"
opened ChimeraX session
> rename #1 DHM
> close #3
> open
> /Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/A1*-AlphaFold_test_30028_A1*/test_30028_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb
Chain information for
test_30028_unrelaxed_rank_001_alphafold2_ptm_model_3_seed_000.pdb #3
---
Chain | Description
A | No description available
Computing secondary structure
> rename #3 A1*
> matchmaker #3 to #2
Computing secondary structure
Parameters
---
Chain pairing | bb
Alignment algorithm | Needleman-Wunsch
Similarity matrix | BLOSUM-62
SS fraction | 0.3
Gap open (HH/SS/other) | 18/18/6
Gap extend | 1
SS matrix | | | H | S | O
---|---|---|---
H | 6 | -9 | -6
S | | 6 | -6
O | | | 4
Iteration cutoff | 2
Matchmaker 8fen, chain A (#2) with A1*, chain A (#3), sequence alignment score
= 1542.4
RMSD between 312 pruned atom pairs is 0.596 angstroms; (across all 325 pairs:
0.914)
> close #2
> save
> "/Users/Hester/ownCloud2/Bioinformatics/Protein_modeling/Maize_DFR/ChimeraX_sessions/Carried
> out using model 3 (best model)/250319_8FEN_DHM_A1*.cxs"
===== Log before crash end =====
Log:
Startup Messages
---
note | available bundle cache has not been initialized yet
UCSF ChimeraX version: 1.9 (2024-12-11)
© 2016-2024 Regents of the University of California. All rights reserved.
How to cite UCSF ChimeraX
OpenGL version: 4.1 Metal - 88.1
OpenGL renderer: Apple M2 Pro
OpenGL vendor: Apple
Python: 3.11.4
Locale: UTF-8
Qt version: PyQt6 6.7.1, Qt 6.7.1
Qt runtime version: 6.7.3
Qt platform: cocoa
Hardware:
Hardware Overview:
Model Name: MacBook Pro
Model Identifier: Mac14,9
Model Number: Z17G00135D/A
Chip: Apple M2 Pro
Total Number of Cores: 10 (6 performance and 4 efficiency)
Memory: 16 GB
System Firmware Version: 10151.140.19
OS Loader Version: 10151.140.19
Software:
System Software Overview:
System Version: macOS 14.6.1 (23G93)
Kernel Version: Darwin 23.6.0
Time since boot: 4 hours, 18 minutes
Graphics/Displays:
Apple M2 Pro:
Chipset Model: Apple M2 Pro
Type: GPU
Bus: Built-In
Total Number of Cores: 16
Vendor: Apple (0x106b)
Metal Support: Metal 3
Displays:
PN-70TA3/B3:
Resolution: 1920 x 1080 (1080p FHD - Full High Definition)
UI Looks like: 1920 x 1080 @ 60.00Hz
Main Display: Yes
Mirror: On
Mirror Status: Master Mirror
Online: Yes
Rotation: Supported
Television: Yes
Color LCD:
Display Type: Built-in Liquid Retina XDR Display
Resolution: 3024 x 1964 Retina
Mirror: On
Mirror Status: Hardware Mirror
Online: Yes
Automatically Adjust Brightness: Yes
Connection Type: Internal
Installed Packages:
alabaster: 1.0.0
anyio: 4.7.0
appdirs: 1.4.4
appnope: 0.1.4
asttokens: 3.0.0
auditwheel: 6.1.0
babel: 2.16.0
beautifulsoup4: 4.12.3
blockdiag: 3.0.0
blosc2: 3.0.0
build: 1.2.1
certifi: 2023.11.17
cftime: 1.6.4.post1
charset-normalizer: 3.4.0
ChimeraX-AddCharge: 1.5.18
ChimeraX-AddH: 2.2.6
ChimeraX-AlignmentAlgorithms: 2.0.2
ChimeraX-AlignmentHdrs: 3.5
ChimeraX-AlignmentMatrices: 2.1
ChimeraX-Alignments: 2.16.1
ChimeraX-AlphaFold: 1.0.1
ChimeraX-AltlocExplorer: 1.1.2
ChimeraX-AmberInfo: 1.0
ChimeraX-Arrays: 1.1
ChimeraX-Atomic: 1.58.8
ChimeraX-AtomicLibrary: 14.1.11
ChimeraX-AtomSearch: 2.0.1
ChimeraX-AxesPlanes: 2.4
ChimeraX-BasicActions: 1.1.2
ChimeraX-BILD: 1.0
ChimeraX-BlastProtein: 3.0.0
ChimeraX-BondRot: 2.0.4
ChimeraX-BugReporter: 1.0.1
ChimeraX-BuildStructure: 2.13.1
ChimeraX-Bumps: 1.0
ChimeraX-BundleBuilder: 1.4.0
ChimeraX-ButtonPanel: 1.0.1
ChimeraX-CageBuilder: 1.0.1
ChimeraX-CellPack: 1.0
ChimeraX-Centroids: 1.4
ChimeraX-ChangeChains: 1.1
ChimeraX-CheckWaters: 1.4
ChimeraX-ChemGroup: 2.0.1
ChimeraX-Clashes: 2.3
ChimeraX-ColorActions: 1.0.5
ChimeraX-ColorGlobe: 1.0
ChimeraX-ColorKey: 1.5.6
ChimeraX-CommandLine: 1.2.5
ChimeraX-ConnectStructure: 2.0.1
ChimeraX-Contacts: 1.0.1
ChimeraX-Core: 1.9
ChimeraX-CoreFormats: 1.2
ChimeraX-coulombic: 1.4.4
ChimeraX-Crosslinks: 1.0
ChimeraX-Crystal: 1.0
ChimeraX-CrystalContacts: 1.0.1
ChimeraX-DataFormats: 1.2.3
ChimeraX-Dicom: 1.2.6
ChimeraX-DistMonitor: 1.4.2
ChimeraX-DockPrep: 1.1.3
ChimeraX-Dssp: 2.0
ChimeraX-EMDB-SFF: 1.0
ChimeraX-ESMFold: 1.0
ChimeraX-FileHistory: 1.0.1
ChimeraX-FunctionKey: 1.0.1
ChimeraX-Geometry: 1.3
ChimeraX-gltf: 1.0
ChimeraX-Graphics: 1.4.1
ChimeraX-Hbonds: 2.5
ChimeraX-Help: 1.3
ChimeraX-HKCage: 1.3
ChimeraX-IHM: 1.1
ChimeraX-ImageFormats: 1.2
ChimeraX-IMOD: 1.0
ChimeraX-IO: 1.0.3
ChimeraX-ItemsInspection: 1.0.1
ChimeraX-IUPAC: 1.0
ChimeraX-KVFinder: 1.2.1
ChimeraX-Label: 1.1.14
ChimeraX-ListInfo: 1.2.2
ChimeraX-Log: 1.2
ChimeraX-LookingGlass: 1.1
ChimeraX-Maestro: 1.9.1
ChimeraX-Map: 1.3
ChimeraX-MapData: 2.0
ChimeraX-MapEraser: 1.0.1
ChimeraX-MapFilter: 2.0.1
ChimeraX-MapFit: 2.0
ChimeraX-MapSeries: 2.1.1
ChimeraX-Markers: 1.0.1
ChimeraX-Mask: 1.0.2
ChimeraX-MatchMaker: 2.1.6
ChimeraX-MCopy: 1.0
ChimeraX-MDcrds: 2.7.2
ChimeraX-MedicalToolbar: 1.1
ChimeraX-Meeting: 1.0.1
ChimeraX-MLP: 1.1.1
ChimeraX-mmCIF: 2.14.2
ChimeraX-MMTF: 2.2
ChimeraX-ModelArchive: 1.0
ChimeraX-Modeller: 1.5.18
ChimeraX-ModelPanel: 1.5
ChimeraX-ModelSeries: 1.0.1
ChimeraX-Mol2: 2.0.3
ChimeraX-Mole: 1.0
ChimeraX-Morph: 1.0.2
ChimeraX-MouseModes: 1.2
ChimeraX-Movie: 1.0
ChimeraX-MutationScores: 1.0
ChimeraX-Neuron: 1.0
ChimeraX-Nifti: 1.2
ChimeraX-NMRSTAR: 1.0.2
ChimeraX-NRRD: 1.2
ChimeraX-Nucleotides: 2.0.3
ChimeraX-OpenCommand: 1.14
ChimeraX-OrthoPick: 1.0.1
ChimeraX-PDB: 2.7.6
ChimeraX-PDBBio: 1.0.1
ChimeraX-PDBLibrary: 1.0.4
ChimeraX-PDBMatrices: 1.0
ChimeraX-PickBlobs: 1.0.1
ChimeraX-Positions: 1.0
ChimeraX-PresetMgr: 1.1.2
ChimeraX-PubChem: 2.2
ChimeraX-ReadPbonds: 1.0.1
ChimeraX-Registration: 1.1.2
ChimeraX-RemoteControl: 1.0
ChimeraX-RenderByAttr: 1.6.2
ChimeraX-RenumberResidues: 1.1
ChimeraX-ResidueFit: 1.0.1
ChimeraX-RestServer: 1.3.1
ChimeraX-RNALayout: 1.0
ChimeraX-RotamerLibMgr: 4.0
ChimeraX-RotamerLibsDunbrack: 2.0
ChimeraX-RotamerLibsDynameomics: 2.0
ChimeraX-RotamerLibsRichardson: 2.0
ChimeraX-SaveCommand: 1.5.1
ChimeraX-SchemeMgr: 1.0
ChimeraX-SDF: 2.0.2
ChimeraX-Segger: 1.0
ChimeraX-Segment: 1.0.1
ChimeraX-Segmentations: 3.5.6
ChimeraX-SelInspector: 1.0
ChimeraX-SeqView: 2.14
ChimeraX-Shape: 1.0.1
ChimeraX-Shell: 1.0.1
ChimeraX-Shortcuts: 1.2.0
ChimeraX-ShowSequences: 1.0.3
ChimeraX-SideView: 1.0.1
ChimeraX-SimilarStructures: 1.0.1
ChimeraX-Smiles: 2.1.2
ChimeraX-SmoothLines: 1.0
ChimeraX-SpaceNavigator: 1.0
ChimeraX-StdCommands: 1.18.1
ChimeraX-STL: 1.0.1
ChimeraX-Storm: 1.0
ChimeraX-StructMeasure: 1.2.1
ChimeraX-Struts: 1.0.1
ChimeraX-Surface: 1.0.1
ChimeraX-SwapAA: 2.0.1
ChimeraX-SwapRes: 2.5
ChimeraX-TapeMeasure: 1.0
ChimeraX-TaskManager: 1.0
ChimeraX-Test: 1.0
ChimeraX-Toolbar: 1.2.3
ChimeraX-ToolshedUtils: 1.2.4
ChimeraX-Topography: 1.0
ChimeraX-ToQuest: 1.0
ChimeraX-Tug: 1.0.1
ChimeraX-UI: 1.41
ChimeraX-Umap: 1.0
ChimeraX-uniprot: 2.3.1
ChimeraX-UnitCell: 1.0.1
ChimeraX-ViewDockX: 1.4.4
ChimeraX-VIPERdb: 1.0
ChimeraX-Vive: 1.1
ChimeraX-VolumeMenu: 1.0.1
ChimeraX-vrml: 1.0
ChimeraX-VTK: 1.0
ChimeraX-WavefrontOBJ: 1.0
ChimeraX-WebCam: 1.0.2
ChimeraX-WebServices: 1.1.4
ChimeraX-Zone: 1.0.1
colorama: 0.4.6
comm: 0.2.2
contourpy: 1.3.1
cxservices: 1.2.3
cycler: 0.12.1
Cython: 3.0.10
debugpy: 1.8.9
decorator: 5.1.1
docutils: 0.21.2
executing: 2.1.0
filelock: 3.15.4
fonttools: 4.55.3
funcparserlib: 2.0.0a0
glfw: 2.8.0
grako: 3.16.5
h11: 0.14.0
h5py: 3.12.1
html2text: 2024.2.26
httpcore: 1.0.7
httpx: 0.28.1
idna: 3.10
ihm: 1.3
imagecodecs: 2024.6.1
imagesize: 1.4.1
ipykernel: 6.29.5
ipython: 8.26.0
ipywidgets: 8.1.5
jedi: 0.19.1
Jinja2: 3.1.4
jupyter_client: 8.6.2
jupyter_core: 5.7.2
jupyterlab_widgets: 3.0.13
kiwisolver: 1.4.7
line_profiler: 4.1.3
lxml: 5.2.2
lz4: 4.3.3
MarkupSafe: 3.0.2
matplotlib: 3.9.2
matplotlib-inline: 0.1.7
msgpack: 1.0.8
ndindex: 1.9.2
nest-asyncio: 1.6.0
netCDF4: 1.6.5
networkx: 3.3
nibabel: 5.2.0
nptyping: 2.5.0
numexpr: 2.10.2
numpy: 1.26.4
openvr: 1.26.701
packaging: 23.2
ParmEd: 4.2.2
parso: 0.8.4
pep517: 0.13.1
pexpect: 4.9.0
pillow: 10.4.0
pip: 24.2
pkginfo: 1.11.1
platformdirs: 4.3.6
prompt_toolkit: 3.0.48
psutil: 6.0.0
ptyprocess: 0.7.0
pure_eval: 0.2.3
py-cpuinfo: 9.0.0
pycollada: 0.8
pydicom: 2.4.4
pyelftools: 0.31
Pygments: 2.18.0
pynmrstar: 3.3.4
pynrrd: 1.0.0
PyOpenGL: 3.1.7
PyOpenGL-accelerate: 3.1.7
pyopenxr: 1.0.3401
pyparsing: 3.2.0
pyproject_hooks: 1.2.0
PyQt6-commercial: 6.7.1
PyQt6-Qt6: 6.7.3
PyQt6-WebEngine-commercial: 6.7.0
PyQt6-WebEngine-Qt6: 6.7.3
PyQt6-WebEngineSubwheel-Qt6: 6.7.3
PyQt6_sip: 13.8.0
python-dateutil: 2.9.0.post0
pytz: 2024.2
pyzmq: 26.2.0
qtconsole: 5.5.2
QtPy: 2.4.2
qtshim: 1.0
RandomWords: 0.4.0
requests: 2.32.3
scipy: 1.14.0
setuptools: 72.1.0
sfftk-rw: 0.8.1
six: 1.16.0
sniffio: 1.3.1
snowballstemmer: 2.2.0
sortedcontainers: 2.4.0
soupsieve: 2.6
Sphinx: 8.0.2
sphinx-autodoc-typehints: 2.2.3
sphinxcontrib-applehelp: 2.0.0
sphinxcontrib-blockdiag: 3.0.0
sphinxcontrib-devhelp: 2.0.0
sphinxcontrib-htmlhelp: 2.1.0
sphinxcontrib-jsmath: 1.0.1
sphinxcontrib-qthelp: 2.0.0
sphinxcontrib-serializinghtml: 2.0.0
stack-data: 0.6.3
superqt: 0.6.3
tables: 3.10.1
tcia_utils: 1.5.1
tifffile: 2024.7.24
tinyarray: 1.2.4
tornado: 6.4.2
traitlets: 5.14.3
typing_extensions: 4.12.2
tzdata: 2024.2
urllib3: 2.2.3
wcwidth: 0.2.13
webcolors: 24.6.0
wheel: 0.43.0
wheel-filename: 1.4.1
widgetsnbextension: 4.0.13
Change History (2)
comment:1 by , 7 months ago
| Component: | Unassigned → Window Toolkit |
|---|---|
| Owner: | set to |
| Platform: | → all |
| Project: | → ChimeraX |
| Status: | new → assigned |
| Summary: | ChimeraX bug report submission → Crash on Mac waking from sleep |
comment:2 by , 7 months ago
| Resolution: | → duplicate |
|---|---|
| Status: | assigned → closed |
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